This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The AOHUPO Membrane Proteomics Initiative (MPI) was established with goals of developing and evaluating technologies for comprehensive profiling of membrane proteomes. The current focus includes multi-laboratory analysis of a membrane standard (MPI Standard) that is a carbonate washed microsomal fraction prepared from the livers of 10-11 week old male C57BL/6J mice [1]. The sample preparation was optimized by comparing the number of proteins predicted to have transmembrane regions that were identified in LC-MS/MS analysis of different preparations. This data was analyzed by four bioinformatics groups in Melbourne, Beijing, Soul, and New York (The Rockefeller University) using different methods. At RU we identified the peptides using X! Tandem and X! Hunter using the mouse IPI databases. A non-redundant list of proteins was created by grouping proteins with overlapping peptides and transmembrane predictions were done with Phobius. After the initial optimization, the carbonate washed microsomal fraction was distributed to 17 laboratories and analyzed with a wide range of mass spectrometric methods. The bioinformatic analysis of this data set is currently ongoing. 1. M. Chung, K. Nakamura, T.W. Jordan, Proteomics 8 (2008) 3920-3923.